Severe autoimmune diseases can only partially be controlled by conventional immunosuppressive treatments. There are over 40 of these diseases including severe lupus, mixed connective tissue disease and multiple sclerosis. In general, these diseases have been considered chronic diseases, but a small percentage of them are aggressive and can lead rapidly to death. Immunosuppressive drugs, particularly corticosteroids, have been the mainstay of therapy, with cytotoxic agents being used in the more difficult to treat cases. Abnormal immune cells, which recognize self as something foreign to be rejected, are responsible for causing the problems related to these diseases. This study proposes to use a combination of high dose chemotherapy, with radiation therapy and the transplantation of blood stem cells depleted of immune cells in order to eliminate those immune cells that react to self, and replace them with a new immune system that does not recognize self as foreign. The risks of these procedures include predominantly those associated with high dose chemotherapy and radiation therapy, with lower risk of severe organ damage, and up to a 5 % chance of transplant of procedure related death. In order to assure that only patients with the appropriate stages of their diseases are referred for this procedure, all referrals must be reviewed by the appropriate academic faculty at Tulane Medical Center including rheumatology, neurology, pediatric immunology and other appropriate groups. In addition, where necessary, outside experts will be called upon to review potential candidates. All requirement of the Tulane Bone Marrow Transplant Program that apply to cancer patients, regarding patients physiologic and psychological functioning, will be applied to patients on this study. Alternative treatments to be offered to the patients will include further use of standard therapies. However, these will be patients who have been felt to have failed standard therapy or other investigational treatments as may become available for those specific disease entities.